Yes, pull the head to seal that area... it's just as much work the other way, harder to reassemble and you're likely to scrape the RTV out from where it needs to be when you put the plate back on.
Did you go with a metal HG or an OEM style composite HG? If you used a composite HG it needs to be replaced.
Don't forget the RTV at the #1 cam caps when you reinstall the valve covers.
I'd install new cam seals and new valve cover seals if you haven't already done so.
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